Human Gene Functions
Time Limit: 1000MS | Memory Limit: 10000K | |
Total Submissions: 21213 | Accepted: 11825 |
Description
It is well known that a human gene can be considered as a sequence, consisting of four nucleotides, which are simply denoted by four letters, A, C, G, and T. Biologists have been interested in identifying human genes and determining their functions, because these can be used to diagnose human diseases and to design new drugs for them.
A human gene can be identified through a series of time-consuming biological experiments, often with the help of computer programs. Once a sequence of a gene is obtained, the next job is to determine its function.
One of the methods for biologists to use in determining the function of a new gene sequence that they have just identified is to search a database with the new gene as a query. The database to be searched stores many gene sequences and their functions – many researchers have been submitting their genes and functions to the database and the database is freely accessible through the Internet.
A database search will return a list of gene sequences from the database that are similar to the query gene.
Biologists assume that sequence similarity often implies functional similarity. So, the function of the new gene might be one of the functions that the genes from the list have. To exactly determine which one is the right one another series of biological experiments will be needed.
Your job is to make a program that compares two genes and determines their similarity as explained below. Your program may be used as a part of the database search if you can provide an efficient one.
Given two genes AGTGATG and GTTAG, how similar are they? One of the methods to measure the similarity
of two genes is called alignment. In an alignment, spaces are inserted, if necessary, in appropriate positions of
the genes to make them equally long and score the resulting genes according to a scoring matrix.
For example, one space is inserted into AGTGATG to result in AGTGAT-G, and three spaces are inserted into GTTAG to result in –GT--TAG. A space is denoted by a minus sign (-). The two genes are now of equal
length. These two strings are aligned:
AGTGAT-G
-GT--TAG
In this alignment, there are four matches, namely, G in the second position, T in the third, T in the sixth, and G in the eighth. Each pair of aligned characters is assigned a score according to the following scoring matrix.
denotes that a space-space match is not allowed. The score of the alignment above is (-3)+5+5+(-2)+(-3)+5+(-3)+5=9.
Of course, many other alignments are possible. One is shown below (a different number of spaces are inserted into different positions):
AGTGATG
-GTTA-G
This alignment gives a score of (-3)+5+5+(-2)+5+(-1) +5=14. So, this one is better than the previous one. As a matter of fact, this one is optimal since no other alignment can have a higher score. So, it is said that the
similarity of the two genes is 14.
Input
The input consists of T test cases. The number of test cases ) (T is given in the first line of the input file. Each test case consists of two lines: each line contains an integer, the length of a gene, followed by a gene sequence. The length of each gene sequence is at least one and does not exceed 100.
Output
The output should print the similarity of each test case, one per line.
Sample Input
2 7 AGTGATG 5 GTTAG 7 AGCTATT 9 AGCTTTAAA
Sample Output
14 21
题意:给定两组序列,要你求出它们的最大相似度,每个字母与其他字母或自身和空格对应都有一个打分,求在这两个字符串中插入空格,让这两个字符串的匹配分数最大
题解:类似与LCS的DP。定义dp[i][j]是对齐到串s1到第i个字符,s2到第j个字符时可获得的最大评分。则动态转移方程很明显为
dp[i][j] = max(dp[i-1][j-1] + score[s1[i]][s2[j]], max(dp[i-1][j] + score[s1[i]][' '], dp[i][j-1] + score[' '][s2[j]])。
第一项理解为s1、s2同时右移一位,不替换空格。第二项为s1替换为空格,而s2没有任何操作,只需要计算dp[i-1][j]+score[s1[i]][' '],第三项同理。
坑的一个点是初始化的问题。可知dp[0][0]=0。而dp[0][j]通过理解状态可知,s1保持而s2对齐到j,需要不断的将s2的字符替换成' '才能达到位置j,所以dp[0][j] = dp[0][j-1] + score[s2[j]][' ']。
关于转移时二三项如何确定替换s1还是s2为空格,可以如下理解:因为要对齐到i,j位置,i-1,j到目标位置需要s1移动一位,只能通过添加空格的方法实现,所以是s1[i]位置添加空格。
程序:
#include<cstring>
#include<algorithm>
#include<queue>
#include<iostream>
#include<cstdio>
#define MAXN 100010
using namespace std;
int score[256][256];
int dp[101][101];
void init_score(){
score['A'-'\0']['A'-'\0'] = 5;
score['C'-'\0']['C'-'\0'] = 5;
score['G'-'\0']['G'-'\0'] = 5;
score['T'-'\0']['T'-'\0'] = 5;
score['A'-'\0']['C'-'\0'] = score['C'-'\0']['A'-'\0'] = -1;
score['A'-'\0']['G'-'\0'] = score['G'-'\0']['A'-'\0'] = -2;
score['A'-'\0']['T'-'\0'] = score['T'-'\0']['A'-'\0'] = -1;
score['A'-'\0'][' '-'\0'] = score[' '-'\0']['A'-'\0'] = -3;
score['C'-'\0']['G'-'\0'] = score['G'-'\0']['C'-'\0'] = -3;
score['C'-'\0']['T'-'\0'] = score['T'-'\0']['C'-'\0'] = -2;
score['C'-'\0'][' '-'\0'] = score[' '-'\0']['C'-'\0'] = -4;
score['G'-'\0']['T'-'\0'] = score['T'-'\0']['G'-'\0'] = -2;
score['G'-'\0'][' '-'\0'] = score[' '-'\0']['G'-'\0'] = -2;
score['T'-'\0'][' '-'\0'] = score[' '-'\0']['T'-'\0'] = -1;
}
int main(){
int t, len1, len2;
char s1[101], s2[101];
init_score();
scanf("%d", &t);
while(t--) {
memset(dp, 0, sizeof(dp));
scanf("%d", &len1);
getchar();
scanf("%s", s1+1);
scanf("%d", &len2);
getchar();
scanf("%s", s2+1);
dp[0][0] = 0;
for (int i = 1;i <= len1;i++) {
dp[i][0] = dp[i-1][0] + score[s1[i]-'\0'][' '-'\0'];
}
for (int i = 1;i <= len2;i++) {
dp[0][i] = dp[0][i-1] + score[s2[i]-'\0'][' '-'\0'];
}
for (int i = 1;i <= len1;i++) {
for (int j = 1;j <= len2;j++) {
dp[i][j] = max(dp[i-1][j-1]+score[s1[i]-'\0'][s2[j]-'\0'], max(dp[i-1][j]+score[s1[i] -'\0'][' '-'\0'], dp[i][j-1]+score[' '-'\0'][s2[j]-'\0']));
}
}
printf("%d\n", dp[len1][len2]);
}
return 0;
}